A Jan. 6 memo to the Navy from acting Deputy Secretary of Defense Christine Fox came after the Pentagon got final 2015 budget guidance from the Obama administration, according to the Navy Times and Bloomberg News, citing unnamed Defense Department sources.

At stake is an originally $37 billion program scheduled to include 52 vessels, nearly a fifth of the U.S. fleet. These next-generation ships are intended to be fast, light and operate in coastal waters with a minimal crew and interchangeable weapons. The first dozen are expected to be assigned to San Diego.

Critics in Congress have questioned the ship line for a few years. They were given ammunition by a 2013 report from the Government Accountability Office that recommended pausing the program until the Navy stabilizes the design and makes more progress in testing weapons packages.

The memo is apparently classified. The 2015 federal budget hasn’t yet been delivered, so there may be room for change.

The littorals are intended to replace three kinds of ships: frigates, mine hunters and coastal patrol boats. They do it via a large open architecture, allowing the Navy to interchangeably plug in anti-mine, anti-submarine and anti-ship weapons packages.

The mine and submarine equipment is still being developed. That’s fueled critics, as have reports of early hull corrosion, the high cost of the early ships and internal Pentagon questions about the ship’s ability to withstand a fight.

But the most significant question is probably whether this ship — fast and able to operate in shallow waters around Asia, but also more fragile than a destroyer — is the right vessel to make up such a large chunk of the 300-ship U.S. fleet some day.

A lot was riding on the recent deployment of the first ship in the class, Freedom, and it gave a mixed performance.

But the ship suffered much-scrutinized breakdowns, including seawater contamination and a steering issue prompted by a broken cable.

The littorals come in two shapes. The Freedom is the single-hulled version built by Lockheed Martin. Besides the Freedom and the Fort Worth, both already in San Diego, the Navy is under contract for 10 more of that style.

The Independence version is an aluminum trimaran, made by Austal. The first, named Independence, is already in the fleet, though yet to deploy, and the Coronado is expected to arrive in San Diego for an April commissioning ceremony.

The Navy has purchased another 10 trimarans, bringing the total number of littorals under contract or built to 24.

Navy officials, including Navy Secretary Ray Mabus in San Diego last week, have continued to defend the littoral ships.

A San Diego NASSCO shipyard worker told Mabus that, as a taxpayer, he was concerned about the littoral ship program. The worker asked Mabus about long-reported plans to cut the number of planned ships.

Mabus responded by praising the ship concept.

“These ships are modular, so you can change weapons systems out. We can design new weapons systems. … They operate great in the littorals, which are a lot of the world’s oceans. Particularly in places like the Pacific, we are really going to need those things,” Mabus said.

“I’m a big fan of the LCS. I think it’s going to be an integral part of the future of the Navy,” the Navy secretary said.

But naval analyst Norman Polmar said it would be a good thing if the Navy stops production at 32 — or even at 24.

“There’s so many problems with them, let’s get them straightened out before we build more,” he said.

The loss of ship numbers will be painful for the Navy, he said, though he added, “It’s bad for the fleet, but hopefully we design and build a more capable ship.”

Vice Adm. Tom Copeman, the San Diego-based commander of naval surface forces in the Pacific, told reporters on a conference call last week that the littoral ships are a good deal for taxpayers.

The Navy intends to deploy the littorals for 18 months at a time, swapping out crews while the ship is at sea. That saves on sailing costs and leaves the ship out on patrol longer.

He compared the costs of operating a destroyer, with a 275-person crew, to a littoral, which operates with a slimmed-down rotating crew of 70.

“I’m not comparing the missions. The two are not designed to do the same mission,” he said. “But the LCS is very, very capable of doing the counter-piracy, sea lines of communication, the theater security and cooperation, HADR (humanitarian assistance and disaster relief) — all the types of missions that our surface Navy spends the vast majority of their time on deployment doing.”

Still, Polmar argues that the littoral ships can’t defend themselves as well as frigates, which they are supposed to replace.

“If you take a littoral combat ship and put it in an area which has two airplanes, it can’t defend itself. It has no anti-air capability,” said the author or co-author of more than 40 books on naval, intelligence and aviation subjects.

Copeman also gave a timeline for when the three weapons packages will be ready.

The Freedom already deployed with the first version of the anti-ship package.

The Independence will do final testing of the anti-mine gear in the fall of 2015.

The final package, anti-submarine weapons, will be tested in 2016 or 2017, Copeman said.